From 77a89670be9722199ad88fae93f2130e53bbfd40 Mon Sep 17 00:00:00 2001 From: Sam Isaacson Date: Sat, 30 Dec 2023 18:30:42 -0500 Subject: [PATCH] warning fixes --- HISTORY.md | 4 +- .../catalyst_functionality/dsl_description.md | 2 +- docs/unpublished/pdes.md | 2 +- .../bifurcation_kit_extension.jl | 10 ++-- src/graphs.jl | 10 ++-- src/latexify_recipes.jl | 2 +- src/networkapi.jl | 2 +- src/reactionsystem.jl | 2 +- src/registered_functions.jl | 5 +- test/dsl/dsl_basics.jl | 8 +-- test/dsl/dsl_model_construction.jl | 2 +- test/dsl/dsl_options.jl | 52 +++++++++---------- test/network_analysis/conservation_laws.jl | 2 +- .../component_based_model_creation.jl | 24 +++++---- .../programmatic_model_expansion.jl | 4 +- 15 files changed, 67 insertions(+), 64 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index d786a47bdd..65a8fd4374 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -55,7 +55,7 @@ plot(bif_dia; xguide="k1", yguide="X") - Updated Bifurcation documentation with respect to this new feature. ## Catalyst 13.5 -- Added a CatalystHomotopyContinuationExtension extension, which exports the `hc_steady_state` function if HomotopyContinuation is exported. `hc_steady_state` finds the steady states of a reaction system using the homotopy continuation method. This feature is only available for julia versions 1.9+. Example: +- Added a CatalystHomotopyContinuationExtension extension, which exports the `hc_steady_state` function if HomotopyContinuation is exported. `hc_steady_state` finds the steady states of a reaction system using the homotopy continuation method. This feature is only available for julia versions 1.9+. Example: ```julia wilhelm_2009_model = @reaction_network begin k1, Y --> 2X @@ -792,7 +792,7 @@ rn = @reaction_network Reversible_Reaction begin k1, A --> B k2, B --> A end k1 k2 -nameof(rn) == :Reversible_Reaction +ModelingToolkit.nameof(rn) == :Reversible_Reaction ``` Note, empty networks can no longer be created with parameters, i.e. only ```julia diff --git a/docs/src/catalyst_functionality/dsl_description.md b/docs/src/catalyst_functionality/dsl_description.md index 70bdbe224b..58308f0578 100644 --- a/docs/src/catalyst_functionality/dsl_description.md +++ b/docs/src/catalyst_functionality/dsl_description.md @@ -426,7 +426,7 @@ We can now simulate the network without providing any initial conditions: ```@example tut2 u0 = [] tspan = (0.0, 10.0) -p = [:p => 2.0, :d => .1, :X0 => 1.0] +p = [:p => 2.0, :d => .1, :X0 => 1.0] oprob = ODEProblem(rn, u0, tspan, p) sol = solve(oprob) plot(sol) diff --git a/docs/unpublished/pdes.md b/docs/unpublished/pdes.md index 794ce2cbaa..40122da7e0 100644 --- a/docs/unpublished/pdes.md +++ b/docs/unpublished/pdes.md @@ -12,7 +12,7 @@ parameters in (Kim et al., J. Chem. Phys., 146, 2017). First we load the packages we'll use ```julia using Catalyst, MethodOfLines, DomainSets, OrdinaryDiffEq, Plots, Random, Distributions -using ModelingToolkit: scalarize, unwrap, operation, nameof, defaults +using ModelingToolkit: scalarize, unwrap, operation, defaults ``` Next let's specify our default parameter values diff --git a/ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl b/ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl index 039038212f..07453151fd 100644 --- a/ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl +++ b/ext/CatalystBifurcationKitExtension/bifurcation_kit_extension.jl @@ -1,12 +1,12 @@ ### Dispatch for BifurcationKit BifurcationProblems ### # Creates a BifurcationProblem, using a ReactionSystem as an input. -function BK.BifurcationProblem(rs::ReactionSystem, u0_bif, ps, bif_par, args...; - plot_var=nothing, record_from_solution=BK.record_sol_default, jac=true, u0=[], kwargs...) +function BK.BifurcationProblem(rs::ReactionSystem, u0_bif, ps, bif_par, args...; + plot_var=nothing, record_from_solution=BK.record_sol_default, jac=true, u0=[], kwargs...) # Converts symbols to symbolics. - (bif_par isa Symbol) && (bif_par = rs.var_to_name[bif_par]) - (plot_var isa Symbol) && (plot_var = rs.var_to_name[plot_var]) + (bif_par isa Symbol) && (bif_par = ModelingToolkit.get_var_to_name(rs)[bif_par]) + (plot_var isa Symbol) && (plot_var = ModelingToolkit.get_var_to_name(rs)[plot_var]) ((u0_bif isa Vector{<:Pair{Symbol,<:Any}}) || (u0_bif isa Dict{Symbol, <:Any})) && (u0_bif = symmap_to_varmap(rs, u0_bif)) ((ps isa Vector{<:Pair{Symbol,<:Any}}) || (ps isa Dict{Symbol, <:Any})) && (ps = symmap_to_varmap(rs, ps)) ((u0 isa Vector{<:Pair{Symbol,<:Any}}) || (u0 isa Dict{Symbol, <:Any})) && (u0 = symmap_to_varmap(rs, u0)) @@ -16,6 +16,6 @@ function BK.BifurcationProblem(rs::ReactionSystem, u0_bif, ps, bif_par, args...; nsys = convert(NonlinearSystem, rs; remove_conserved=true, defaults=Dict(u0)) # Makes BifurcationProblem (this call goes through the ModelingToolkit-based BifurcationKit extension). - return BK.BifurcationProblem(nsys, u0_bif, ps, bif_par, args...; plot_var=plot_var, + return BK.BifurcationProblem(nsys, u0_bif, ps, bif_par, args...; plot_var=plot_var, record_from_solution=record_from_solution, jac=jac, kwargs...) end \ No newline at end of file diff --git a/src/graphs.jl b/src/graphs.jl index 5527e99875..8229131051 100644 --- a/src/graphs.jl +++ b/src/graphs.jl @@ -1,7 +1,7 @@ ####################################################################### # Contains code from Catlab.jl: # https://raw.githubusercontent.com/AlgebraicJulia/Catlab.jl/master/src/graphics/Graphviz.jl -# +# # That license for that code is: # # The MIT License @@ -275,7 +275,7 @@ const edge_attrs = Attributes(:splines => "splines") function edgify(δ, i, reverse::Bool) attr = Attributes() return map(δ) do p - val = String(p[1].f.name) + val = String(getname(p[1])) weight = "$(p[2])" attr = Attributes(:label => weight, :labelfontsize => "6") return Edge(reverse ? ["rx_$i", "$val"] : @@ -289,7 +289,7 @@ function edgifyrates(rxs, specs) for (i, rx) in enumerate(rxs) deps = rx.rate isa Number ? Any[] : get_variables(rx.rate, specs) for dep in deps - val = String(dep.f.name) + val = String(getname(dep)) attr = Attributes(:color => "#d91111", :style => "dashed") e = Edge(["$val", "rx_$i"], attr) push!(es, e) @@ -324,7 +324,7 @@ end complexgraph(rn::ReactionSystem; complexdata=reactioncomplexes(rn)) Creates a Graphviz graph of the [`ReactionComplex`](@ref)s in `rn`. Reactions -correspond to arrows and reaction complexes to blue circles. +correspond to arrows and reaction complexes to blue circles. Notes: - Black arrows from complexes to complexes indicate reactions whose rate is a @@ -389,7 +389,7 @@ Notes: function Graph(rn::ReactionSystem) rxs = reactions(rn) specs = species(rn) - statenodes = [Node(string(s.f.name), + statenodes = [Node(string(getname(s)), Attributes(:shape => "circle", :color => "#6C9AC3")) for s in specs] transnodes = [Node(string("rx_$i"), Attributes(:shape => "point", :color => "#E28F41", :width => ".1")) diff --git a/src/latexify_recipes.jl b/src/latexify_recipes.jl index f14929784f..a5601d5185 100644 --- a/src/latexify_recipes.jl +++ b/src/latexify_recipes.jl @@ -118,7 +118,7 @@ function chemical_arrows(rn::ReactionSystem; expand = true, rxs = reactions(rn) nonrxs = filter(eq -> eq isa Equation, equations(rn)) if isempty(rxs) && isempty(nonrxs) - latexstr = Latexify.LaTeXString("ReactionSystem $(nameof(rn)) has no reactions or equations.") + latexstr = Latexify.LaTeXString("ReactionSystem $(ModelingToolkit.nameof(rn)) has no reactions or equations.") Latexify.COPY_TO_CLIPBOARD && clipboard(latexstr) return latexstr end diff --git a/src/networkapi.jl b/src/networkapi.jl index 8853d8d379..910703e88a 100644 --- a/src/networkapi.jl +++ b/src/networkapi.jl @@ -1285,7 +1285,7 @@ conservedquantities(state, cons_laws) = cons_laws * state function conservationlaw_errorcheck(rs, pre_varmap) vars_with_vals = Set(p[1] for p in pre_varmap) any(s -> s in vars_with_vals, species(rs)) && return - isempty(conservedequations(Catalyst.flatten(rs))) || + isempty(conservedequations(Catalyst.flatten(rs))) || error("The system has conservation laws but initial conditions were not provided for some species.") end diff --git a/src/reactionsystem.jl b/src/reactionsystem.jl index 4fdb99f3ee..83387ef921 100644 --- a/src/reactionsystem.jl +++ b/src/reactionsystem.jl @@ -1438,7 +1438,7 @@ Notes: """ function Base.convert(::Type{<:JumpSystem}, rs::ReactionSystem; name = nameof(rs), combinatoric_ratelaws = get_combinatoric_ratelaws(rs), - remove_conserved = nothing, checks = false, + remove_conserved = nothing, checks = false, default_u0 = Dict(), default_p = Dict(), defaults = _merge(Dict(default_u0), Dict(default_p)), kwargs...) spatial_convert_err(rs::ReactionSystem, JumpSystem) diff --git a/src/registered_functions.jl b/src/registered_functions.jl index 8a5b2f821c..33134aaf86 100644 --- a/src/registered_functions.jl +++ b/src/registered_functions.jl @@ -142,6 +142,7 @@ function expand_registered_functions(eq::Equation) end # If applied to a ReactionSystem, applied function to all Reactions and other Equations, and return updated system. function expand_registered_functions(rs::ReactionSystem) - rs = @set rs.eqs = [Catalyst.expand_registered_functions(eq) for eq in rs.eqs] - return @set rs.rxs = [Catalyst.expand_registered_functions(rx) for rx in rs.rxs] + @set! rs.eqs = [Catalyst.expand_registered_functions(eq) for eq in get_eqs(rs)] + @set! rs.rxs = [Catalyst.expand_registered_functions(rx) for rx in get_rxs(rs)] + return rs end diff --git a/test/dsl/dsl_basics.jl b/test/dsl/dsl_basics.jl index 78fadfcacc..1a9af26905 100644 --- a/test/dsl/dsl_basics.jl +++ b/test/dsl/dsl_basics.jl @@ -2,7 +2,7 @@ ### Fetch Packages and Set Global Variables ### -using Catalyst +using Catalyst, ModelingToolkit @variables t ### Naming Tests ### @@ -12,14 +12,14 @@ let @species A(t) rx = Reaction(k, [A], nothing) function rntest(rn, name) - @test nameof(rn) == name + @test ModelingToolkit.nameof(rn) == name @test isequal(species(rn)[1], ModelingToolkit.unwrap(A)) @test isequal(parameters(rn)[1], ModelingToolkit.unwrap(k)) @test reactions(rn)[1] == rx end function emptyrntest(rn, name) - @test nameof(rn) == name + @test ModelingToolkit.nameof(rn) == name @test numreactions(rn) == 0 @test numspecies(rn) == 0 @test numreactionparams(rn) == 0 @@ -42,7 +42,7 @@ let @parameters k k, A --> 0 end - rntest(rn, nameof(rn)) + rntest(rn, ModelingToolkit.nameof(rn)) function makern(; name) @reaction_network $name begin diff --git a/test/dsl/dsl_model_construction.jl b/test/dsl/dsl_model_construction.jl index a5f197bd0b..fea9efcc3a 100644 --- a/test/dsl/dsl_model_construction.jl +++ b/test/dsl/dsl_model_construction.jl @@ -3,7 +3,7 @@ # Fetch packages. using DiffEqBase, Catalyst, Random, Test using ModelingToolkit: operation, istree, get_states, get_ps, get_eqs, get_systems, - get_iv + get_iv, nameof # Sets rnd number. using StableRNGs diff --git a/test/dsl/dsl_options.jl b/test/dsl/dsl_options.jl index 3a52d821b8..f6d177918d 100644 --- a/test/dsl/dsl_options.jl +++ b/test/dsl/dsl_options.jl @@ -49,48 +49,48 @@ let (k1, k2), A <--> B end - n1 = @reaction_network name begin (k1, k2), A <--> B end - n2 = @reaction_network name begin + n1 = @reaction_network rnname begin (k1, k2), A <--> B end + n2 = @reaction_network rnname begin @parameters k1 k2 (k1, k2), A <--> B end - n3 = @reaction_network name begin + n3 = @reaction_network rnname begin @species A(t) B(t) (k1, k2), A <--> B end - n4 = @reaction_network name begin + n4 = @reaction_network rnname begin @parameters k1 k2 @species A(t) B(t) (k1, k2), A <--> B end - n5 = @reaction_network name begin + n5 = @reaction_network rnname begin (k1, k2), A <--> B @parameters k1 k2 end - n6 = @reaction_network name begin + n6 = @reaction_network rnname begin (k1, k2), A <--> B @species A(t) B(t) end - n7 = @reaction_network name begin + n7 = @reaction_network rnname begin (k1, k2), A <--> B @parameters k1 k2 @species A(t) B(t) end - n8 = @reaction_network name begin + n8 = @reaction_network rnname begin @parameters begin k1 k2 end (k1, k2), A <--> B end - n9 = @reaction_network name begin + n9 = @reaction_network rnname begin @species begin A(t) B(t) end (k1, k2), A <--> B end - n10 = @reaction_network name begin + n10 = @reaction_network rnname begin @parameters begin k1 k2 @@ -104,7 +104,7 @@ let @test all(==(n1), (n2, n3, n4, n5, n6, n7, n8, n9, n10)) end -# Tests that when either @species or @parameters is given, the other is infered properly. +# Tests that when either @species or @parameters is given, the other is infered properly. let rn1 = @reaction_network begin k*X, A + B --> 0 @@ -222,16 +222,16 @@ end ##Checks that some created networks are identical. let - rn12 = @reaction_network name begin (k1, k2), A <--> B end - rn13 = @reaction_network name begin + rn12 = @reaction_network rnname begin (k1, k2), A <--> B end + rn13 = @reaction_network rnname begin @parameters k1 k2 (k1, k2), A <--> B end - rn14 = @reaction_network name begin + rn14 = @reaction_network rnname begin @species A(t) B(t) (k1, k2), A <--> B end - rn15 = @reaction_network name begin + rn15 = @reaction_network rnname begin @parameters k1 k2 @species A(t) B(t) (k1, k2), A <--> B @@ -239,16 +239,16 @@ let @test all(==(rn12), (rn13, rn14, rn15)) end -# Checks that the rights things are put in vectors. +# Checks that the rights things are put in vectors. let - rn18 = @reaction_network name begin + rn18 = @reaction_network rnname begin @parameters p d1 d2 @species A(t) B(t) p, 0 --> A 1, A --> B (d1, d2), (A, B) --> 0 end - rn19 = @reaction_network name begin + rn19 = @reaction_network rnname begin p, 0 --> A 1, A --> B (d1, d2), (A, B) --> 0 @@ -263,21 +263,21 @@ let @test isequal(species(rn18)[1], A) @test isequal(species(rn18)[2], B) - rn20 = @reaction_network name begin + rn20 = @reaction_network rnname begin @species X(t) @parameters S mm(X,v,K), 0 --> Y (k1,k2), 2Y <--> Y2 d*Y, S*(Y2+Y) --> 0 end - rn21 = @reaction_network name begin + rn21 = @reaction_network rnname begin @species X(t) Y(t) Y2(t) @parameters v K k1 k2 d S mm(X,v,K), 0 --> Y (k1,k2), 2Y <--> Y2 d*Y, S*(Y2+Y) --> 0 end - rn22 = @reaction_network name begin + rn22 = @reaction_network rnname begin @species X(t) Y2(t) @parameters d k1 mm(X,v,K), 0 --> Y @@ -291,9 +291,9 @@ let @test issetequal(species(rn22), [X Y Y2]) end -# Tests that defaults work. +# Tests that defaults work. let - rn26 = @reaction_network name begin + rn26 = @reaction_network rnname begin @parameters p=1.0 d1 d2=5 @species A(t) B(t)=4 p, 0 --> A @@ -301,7 +301,7 @@ let (d1, d2), (A, B) --> 0 end - rn27 = @reaction_network name begin + rn27 = @reaction_network rnname begin @parameters p1=1.0 p2=2.0 k1=4.0 k2=5.0 v=8.0 K=9.0 n=3 d=10.0 @species X(t)=4.0 Y(t)=3.0 X2Y(t)=2.0 Z(t)=1.0 (p1,p2), 0 --> (X,Y) @@ -312,7 +312,7 @@ let u0_27 = [] p_27 = [] - rn28 = @reaction_network name begin + rn28 = @reaction_network rnname begin @parameters p1=1.0 p2 k1=4.0 k2 v=8.0 K n=3 d @species X(t)=4.0 Y(t) X2Y(t) Z(t)=1.0 (p1,p2), 0 --> (X,Y) @@ -324,7 +324,7 @@ let p_28 = symmap_to_varmap(rn28, [:Y=>3.0, :X2Y=>2.0]) defs28 = Dict(Iterators.flatten((u0_28, p_28))) - rn29 = @reaction_network name begin + rn29 = @reaction_network rnname begin @parameters p1 p2 k1 k2 v K n d @species X(t) Y(t) X2Y(t) Z(t) (p1,p2), 0 --> (X,Y) diff --git a/test/network_analysis/conservation_laws.jl b/test/network_analysis/conservation_laws.jl index ccba38fca9..8557c5b50d 100644 --- a/test/network_analysis/conservation_laws.jl +++ b/test/network_analysis/conservation_laws.jl @@ -63,7 +63,7 @@ let cons_laws = conservationlaws(rn) cons_eqs = conservedequations(rn) cons_laws_constants = conservationlaw_constants(rn) - conserved_quantity = conservedquantities(cons_laws[1, :], rn.states[1]) + conserved_quantity = conservedquantities(cons_laws[1, :], states(rn)[1]) @test sum(cons_laws) == 4 @test size(cons_laws) == (2, 4) diff --git a/test/programmatic_model_creation/component_based_model_creation.jl b/test/programmatic_model_creation/component_based_model_creation.jl index a832d0072b..972f990c5b 100644 --- a/test/programmatic_model_creation/component_based_model_creation.jl +++ b/test/programmatic_model_creation/component_based_model_creation.jl @@ -1,6 +1,8 @@ #! format: off using ModelingToolkit, Catalyst, LinearAlgebra, OrdinaryDiffEq, Test using SciMLNLSolve +using ModelingToolkit: nameof + ### Run Tests ### @@ -453,7 +455,7 @@ let end # Tests that conversion with defaults works for a composed model. -let +let rn1 = @reaction_network rn1 begin @parameters p=1.0 r=2.0 @species X(t) = 3.0 Y(t) = 4.0 @@ -469,15 +471,15 @@ let composed_reaction_system = compose(rn1, [rn2]) osys = convert(ODESystem, composed_reaction_system) parameters(osys)[1].metadata - - osys.defaults + + defs = ModelingToolkit.defaults(osys) @unpack p, r, X, Y = rn1 - osys.defaults[p] == 1.0 - osys.defaults[r] == 2.0 - osys.defaults[X] == 3.0 - osys.defaults[Y] == 4.0 - osys.defaults[rn2.p] == 10.0 - osys.defaults[rn2.q] == 20.0 - osys.defaults[rn2.X] == 30.0 - osys.defaults[rn2.Z] == 40.0 + defs[p] == 1.0 + defs[r] == 2.0 + defs[X] == 3.0 + defs[Y] == 4.0 + defs[rn2.p] == 10.0 + defs[rn2.q] == 20.0 + defs[rn2.X] == 30.0 + defs[rn2.Z] == 40.0 end \ No newline at end of file diff --git a/test/programmatic_model_creation/programmatic_model_expansion.jl b/test/programmatic_model_creation/programmatic_model_expansion.jl index bc60ebc524..bb8b54904a 100644 --- a/test/programmatic_model_creation/programmatic_model_expansion.jl +++ b/test/programmatic_model_creation/programmatic_model_expansion.jl @@ -4,7 +4,7 @@ # Fetch packages. using Catalyst, Test -using ModelingToolkit: get_ps, get_states, get_eqs, get_systems, get_iv +using ModelingToolkit: get_ps, get_states, get_eqs, get_systems, get_iv, getname, nameof # Sets rnd number. using StableRNGs @@ -42,7 +42,7 @@ let @test nameof(iv) == :t @test length(get_states(empty_network_2)) == 0 @test length(ps) == 5 - @test all(getproperty.(ps, :name) .== [:p1, :p2, :p3, :p4, :p5]) + @test all(getname.(ps) .== [:p1, :p2, :p3, :p4, :p5]) end # Tests accessing parameters and species added with network API.